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- PDB-6f38: Cryo-EM structure of two dynein tail domains bound to dynactin an... -

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Entry
Database: PDB / ID: 6f38
TitleCryo-EM structure of two dynein tail domains bound to dynactin and HOOK3
Components
  • (Cytoplasmic dynein 1 ...) x 3
  • (Dynactin Subunit ...) x 12
  • ARP1 actin related protein 1 homolog A
  • Actin related protein 10 homolog
  • Actin, cytoplasmic 1
  • Capping protein (Actin filament) muscle Z-line, alpha 1
  • Dynactin 6
  • Dynein light chain roadblock-type 1
  • F-actin capping protein beta subunit
  • HOOK3
KeywordsMOTOR PROTEIN / TDH / DDH / Complex / dynein/dynactin/HOOK3
Function / homology
Function and homology information


RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / retrograde axonal transport of mitochondrion ...RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / retrograde axonal transport of mitochondrion / UCH proteinases / Gap junction degradation / Formation of annular gap junctions / RHOF GTPase cycle / Clathrin-mediated endocytosis / Formation of the dystrophin-glycoprotein complex (DGC) / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / dynactin complex / Recruitment of mitotic centrosome proteins and complexes / transport along microtubule / visual behavior / F-actin capping protein complex / WASH complex / dynein light chain binding / dynein heavy chain binding / cellular response to cytochalasin B / ciliary tip / regulation of transepithelial transport / positive regulation of intracellular transport / Intraflagellar transport / morphogenesis of a polarized epithelium / regulation of metaphase plate congression / establishment of spindle localization / protein localization to adherens junction / postsynaptic actin cytoskeleton / structural constituent of postsynaptic actin cytoskeleton / positive regulation of spindle assembly / Tat protein binding / barbed-end actin filament capping / Neutrophil degranulation / dense body / coronary vasculature development / apical protein localization / adherens junction assembly / dynein complex / regulation of cell morphogenesis / COPI-independent Golgi-to-ER retrograde traffic / retrograde axonal transport / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / tight junction / P-body assembly / minus-end-directed microtubule motor activity / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / dynein light intermediate chain binding / microtubule motor activity / cytoplasmic dynein complex / aorta development / COPI-mediated anterograde transport / centrosome localization / ventricular septum development / dynein intermediate chain binding / regulation of norepinephrine uptake / nuclear migration / transporter regulator activity / apical junction complex / microtubule-based movement / nitric-oxide synthase binding / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / cortical cytoskeleton / dynein complex binding / regulation of synaptic vesicle endocytosis / brush border / kinesin binding / positive regulation of double-strand break repair via homologous recombination / microtubule-based process / regulation of protein localization to plasma membrane / cytoplasmic microtubule / COPI-mediated anterograde transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule organization / axon cytoplasm / cytoskeleton organization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / stress granule assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / calyx of Held / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / regulation of mitotic spindle organization
Similarity search - Function
Dynein 1 light intermediate chain / Dynamitin / : / Dynamitin / Dynactin subunit 6 / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein family light intermediate chain / Dynein light intermediate chain (DLIC) / Dynein light chain roadblock-type 1/2 ...Dynein 1 light intermediate chain / Dynamitin / : / Dynamitin / Dynactin subunit 6 / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein family light intermediate chain / Dynein light intermediate chain (DLIC) / Dynein light chain roadblock-type 1/2 / Dynactin subunit 5 / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / : / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / : / Dynein heavy chain, ATPase lid domain / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, linker / Dynein heavy chain, AAA module D4 / Dynein heavy chain, coiled coil stalk / Dynein heavy chain / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Dynein heavy chain, ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Dynein heavy chain AAA lid domain superfamily / Dynein heavy chain, domain 2, N-terminal / Dynein heavy chain, linker, subdomain 3 / Dynein heavy chain, AAA1 domain, small subdomain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, N-terminal region 2 / Hydrolytic ATP binding site of dynein motor region / Microtubule-binding stalk of dynein motor / P-loop containing dynein motor region D4 / ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / WD domain, G-beta repeat / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Dynactin subunit 5 / F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta / Dynactin subunit 6 / Dynactin subunit 2 / Dynactin subunit 2 / Alpha-centractin / Actin-related protein 10 ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Dynactin subunit 5 / F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta / Dynactin subunit 6 / Dynactin subunit 2 / Dynactin subunit 2 / Alpha-centractin / Actin-related protein 10 / Cytoplasmic dynein 1 light intermediate chain 2 / Cytoplasmic dynein 1 intermediate chain 2 / Cytoplasmic dynein 1 heavy chain 1 / Actin, cytoplasmic 1 / Dynein light chain roadblock-type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsLau, C.K. / Urnavicius, L. / Elshenawy, M.M. / Morales-Rios, E. / Motz, C. / Yildiz, A. / Carter, A.P.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_A025_1011 United Kingdom
Wellcome TrustWT100387 United Kingdom
CitationJournal: Nature / Year: 2018
Title: Cryo-EM shows how dynactin recruits two dyneins for faster movement.
Authors: Linas Urnavicius / Clinton K Lau / Mohamed M Elshenawy / Edgar Morales-Rios / Carina Motz / Ahmet Yildiz / Andrew P Carter /
Abstract: Dynein and its cofactor dynactin form a highly processive microtubule motor in the presence of an activating adaptor, such as BICD2. Different adaptors link dynein and dynactin to distinct cargoes. ...Dynein and its cofactor dynactin form a highly processive microtubule motor in the presence of an activating adaptor, such as BICD2. Different adaptors link dynein and dynactin to distinct cargoes. Here we use electron microscopy and single-molecule studies to show that adaptors can recruit a second dynein to dynactin. Whereas BICD2 is biased towards recruiting a single dynein, the adaptors BICDR1 and HOOK3 predominantly recruit two dyneins. We find that the shift towards a double dynein complex increases both the force and speed of the microtubule motor. Our 3.5 Å resolution cryo-electron microscopy reconstruction of a dynein tail-dynactin-BICDR1 complex reveals how dynactin can act as a scaffold to coordinate two dyneins side-by-side. Our work provides a structural basis for understanding how diverse adaptors recruit different numbers of dyneins and regulate the motile properties of the dynein-dynactin transport machine.
History
DepositionNov 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 9, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _pdbx_database_status.process_site
Revision 1.4Dec 11, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: ARP1 actin related protein 1 homolog A
B: ARP1 actin related protein 1 homolog A
C: ARP1 actin related protein 1 homolog A
D: ARP1 actin related protein 1 homolog A
E: ARP1 actin related protein 1 homolog A
F: ARP1 actin related protein 1 homolog A
G: ARP1 actin related protein 1 homolog A
H: Actin, cytoplasmic 1
I: ARP1 actin related protein 1 homolog A
J: Actin related protein 10 homolog
K: Capping protein (Actin filament) muscle Z-line, alpha 1
L: F-actin capping protein beta subunit
M: Dynactin Subunit 2
N: Dynactin Subunit 2
O: Dynactin Subunit 3
P: Dynactin Subunit 3
Q: Dynactin Subunit 2
R: Dynactin Subunit 2
U: Dynactin 6
V: Dynactin subunit 5
X: HOOK3
Y: Dynactin Subunit 4
Z: Dynactin Subunit 1
a: Dynactin subunit 2
b: Dynactin subunit 2
c: Dynactin subunit 2
d: Dynactin subunit 2
e: Cytoplasmic dynein 1 heavy chain 1
f: Cytoplasmic dynein 1 heavy chain 1
g: Cytoplasmic dynein 1 intermediate chain 2
h: Cytoplasmic dynein 1 intermediate chain 2
i: Cytoplasmic dynein 1 light intermediate chain 2
j: Cytoplasmic dynein 1 light intermediate chain 2
k: Dynein light chain roadblock-type 1
l: Dynein light chain roadblock-type 1
m: Cytoplasmic dynein 1 heavy chain 1
n: Cytoplasmic dynein 1 heavy chain 1
o: Cytoplasmic dynein 1 intermediate chain 2
p: Cytoplasmic dynein 1 intermediate chain 2
q: Cytoplasmic dynein 1 light intermediate chain 2
r: Cytoplasmic dynein 1 light intermediate chain 2
s: Dynein light chain roadblock-type 1
t: Dynein light chain roadblock-type 1
x: HOOK3
z: Dynactin Subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,967,09055
Polymers1,962,73845
Non-polymers4,35210
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Sample was cross-linked for stability using glutaraldehyde (0.0125% v/v)
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 8 types, 19 molecules ABCDEFGIHJKLUXxklst

#1: Protein
ARP1 actin related protein 1 homolog A


Mass: 42670.688 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Details: ADP: Adenosine Diphosphate / Source: (natural) Sus scrofa (pig) / References: UniProt: F2Z5G5
#2: Protein Actin, cytoplasmic 1 / Beta-actin


Mass: 41782.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ATP: Adenosine triphosphate / Source: (natural) Sus scrofa (pig) / References: UniProt: Q6QAQ1
#3: Protein Actin related protein 10 homolog


Mass: 43203.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ADP: Adenosine diphosphate / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LHK5
#4: Protein Capping protein (Actin filament) muscle Z-line, alpha 1 / F-actin capping protein alpha 1 subunit / F-actin capping protein subunit alpha 1


Mass: 33059.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0PFK5
#5: Protein F-actin capping protein beta subunit / F-actin-capping protein subunit beta / F-actin-capping protein subunit beta isoform 1


Mass: 30669.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A9XFX6
#10: Protein Dynactin 6


Mass: 20703.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: D0G6S1
#12: Protein HOOK3


Mass: 18996.346 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#22: Protein
Dynein light chain roadblock-type 1 / Bithoraxoid-like protein / BLP / Dynein light chain 2A / cytoplasmic / Dynein-associated protein ...Bithoraxoid-like protein / BLP / Dynein light chain 2A / cytoplasmic / Dynein-associated protein Km23 / Roadblock domain-containing protein 1


Mass: 10934.576 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNLRB1, BITH, DNCL2A, DNLC2A, ROBLD1, HSPC162 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NP97

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Dynactin Subunit ... , 12 types, 14 molecules MNOPQRVYZabcdz

#6: Protein Dynactin Subunit 2


Mass: 49974.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#7: Protein Dynactin Subunit 2


Mass: 52442.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#8: Protein Dynactin Subunit 3


Mass: 5549.833 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#9: Protein Dynactin Subunit 2


Mass: 7422.140 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#11: Protein Dynactin subunit 5


Mass: 20150.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZK88
#13: Protein Dynactin Subunit 4


Mass: 22485.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#14: Protein Dynactin Subunit 1


Mass: 4443.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#15: Protein Dynactin subunit 2


Mass: 7578.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SKF9
#16: Protein Dynactin subunit 2


Mass: 10147.034 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SKF9
#17: Protein/peptide Dynactin subunit 2


Mass: 5551.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SL58
#18: Protein/peptide Dynactin subunit 2


Mass: 3239.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SL58, UniProt: F1SKF9*PLUS
#23: Protein Dynactin Subunit 1


Mass: 4528.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)

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Cytoplasmic dynein 1 ... , 3 types, 12 molecules efmnghopijqr

#19: Protein
Cytoplasmic dynein 1 heavy chain 1 / Cytoplasmic dynein heavy chain 1 / Dynein heavy chain / cytosolic


Mass: 168318.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1H1, DHC1, DNCH1, DNCL, DNECL, DYHC, KIAA0325 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14204
#20: Protein
Cytoplasmic dynein 1 intermediate chain 2 / Cytoplasmic dynein intermediate chain 2 / Dynein intermediate chain 2 / cytosolic / DH IC-2


Mass: 68442.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1I2, DNCI2, DNCIC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13409
#21: Protein
Cytoplasmic dynein 1 light intermediate chain 2 / Dynein light intermediate chain 2 / cytosolic / LIC-2 / LIC53/55


Mass: 54173.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1LI2, DNCLI2, LIC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43237

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Non-polymers , 2 types, 10 molecules

#24: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#25: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex of two dynein tail domains bound to dynactin and HOOK3COMPLEX#1-#19, #21, #20, #22-#230MULTIPLE SOURCES
2DynactinCOMPLEX#1-#11, #13-#18, #231NATURAL
3DyneinCOMPLEX#19-#221RECOMBINANT
4HOOK3COMPLEX#121RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Sus scrofa (pig)9823
23Homo sapiens (human)9606
34Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Spooptera frugiperda7108
24Spooptera frugiperda7108
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 45 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_2919: / Classification: refinement
EM software
IDNameCategory
4GctfCTF correction
7Cootmodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23407 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Corellation Coefficient
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00668772
ELECTRON MICROSCOPYf_angle_d1.42295758
ELECTRON MICROSCOPYf_dihedral_angle_d2.71140269
ELECTRON MICROSCOPYf_chiral_restr0.06113255
ELECTRON MICROSCOPYf_plane_restr0.00927464

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